USDA releases sequences of 150 avian flu viruses

Jun 2, 2008 (CIDRAP News) – The US Department of Agriculture (USDA) recently announced the release of complete genetic data for 150 avian influenza viruses in an effort to connect genetic information with the biological effects of the viruses and to improve diagnostic tests.

USDA announced the release of the viral genetic sequences to GenBank, the National Institute of Health's public genetic sequence database, on May 30. The viruses, mostly from North America, represent nearly all avian flu subtypes and were collected from the 1930s to the present, according to David Suarez, research leader of the Exotic and Emerging Avian Viral Diseases Research Unit at the Southeast Poultry Research Laboratory (SEPRL) in Athens, Ga. The lab is part of the USDA's Agricultural Research Service.

"This sequence information, deciphered by our large team, will help researchers better understand virus biology and improve diagnostic tests for avian influenza viruses," Suarez said in a USDA news release. He said SEPRL's goal is to fully sequence 900 avian flu viruses.

The viruses in the latest release include both poultry and wild-bird isolates from many countries, but mostly from North American poultry, Suarez told CIDRAP News.

"Probably the largest number of them have come from live-bird market surveillance, primarily conducted by APHIS [the Animal and Plant Health Inspection Service], through our collaboration with the National Veterinary Services Laboratory," he said.

Researchers at the University of Georgia, Ohio State University, and the University of Alaska-Fairbanks also contributed isolates for the project, the USDA said.

The sequence data includes about 10 or 15 viruses collected in the 1930s and held at the USDA laboratory at Plum Island, New York, Suarez reported. There are also isolates from the 1970s and 1980s, but most are from the 1990s and 2000s, he said.

"Some of these viruses are not necessarily very recent viruses, but we're going back and systematically getting more information on these earlier isolates," Suarez said. "Ultimately we hope to link the phenotype with the genotype. This is a big first step to get the genetic information available. As we go back and get more biological information, we hope ultimately to make a coherent story out of that."

Most avian flu subtypes are included in the 150 isolates, Suarez said. Influenza viruses are named for which of the 16 types of hemagglutinin (H) and 9 types of neuraminidase (N) they carry.

The highest percentages of the viruses are H5 and H7 subtypes, but the isolates also include most of the other hemagglutinin types, Suarez said. "Probably the only ones we don't have are [H]14 or [H]15," he added.

The genetic sequencing project is coupled with research on the biological effects of the viruses, Suarez said. That involves inoculating chickens, ducks, and turkeys with the pathogens and observing to what extent they replicate and cause disease.

Suarez said having more genetic sequences available should make it possible to improve diagnostic tests, especially polymerase chain reaction (PCR) tests, for avian flu. PCR testing relies on the use of short man-made pieces of DNA (primers) that match DNA sequences on the ends of a gene of a virus or organism being tested for.

"In the past some of the diagnostic tests haven't worked as well as expected because of missing sequences," Suarez said.

After the viral isolates were prepared at the USDA lab, sequencing of the viral genes was done by SeqWright Corp. in Houston, according to the USDA news release. SEPRL then reviewed and annotated the resulting information before releasing it to GenBank.